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I have had problems to generate pixel art for a game where units are of specific sizes such as 55x55 (not geometry but by pixels i.e. 55 pixels by 55 pixels). I have tried Gimp where I have misread many-times the sizes with the select tool -- it is irritating to get a bit too distorted size. Then I have used Inkscape that works actually quite good -- you generate the vector-image and select it and then you go to "Export to bitmap" where you can specify the size (this same feature is probably also in Blender, probably as easy). Anyway I am looking for something more powerful like having helper color-palettes easily or automatically-done perhaps like here with Gimp. I can find a variety of tools mentioning pixels but I hope you to point out the best before trying all of them.

$ apt-cache search pixel|wc
     99     861    6029

Perhaps related

  1. http://graphicdesign.stackexchange.com/questions/7860/how-can-i-adjoin-images-with-imagemagick-for-pixel-art

  2. Some example with Photoshop here, create pixel art by reusing basic things such as hands, hairs and bodies (create separate files for them).

  3. A pixel-art competition here.

  4. Using blender for generating stuff here programmatically.

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Take a look at mtpaint, which is a quite handy Paint-like app which was designed for drawing pixel art:

mtPaint is a painting program which Mark Tyler developed from scratch so he could easily create pixel art and manipulate digital photos.

mtpaint screenshot

As for automatic generation, likely you will have to develop something using ImageMagick or another programming language.

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